On the website of remodel
It is said:
"By replacing the "." to "E", "L", "H", or "D", Remodel will build residues with secondary structure of extended strand, loop, helix, or random, respectively."
Can I ask
1) Why there is no beta-sheet?
2) The "random" means "random coil"?
3) Is there a way that I do not need to specify the secondary structure and let Remodel to choose the best one?
When I use "L", it is successful. But when I change it to "D", I am told (attached):
ERROR:: Exit from: src/core/kinematics/FoldTree.cc line: 876
[ERROR] Exception caught by JobDistributor for job 4KMT_FullAtom_missding_residue_in_HC_0001
[ERROR] EXCN_utility_exit has been thrown from: src/core/kinematics/FoldTree.cc line: 876
Can I ask why?
Thank you very much.